Passing a seawater challenge test is not indicative of hatchery-reared Atlantic salmon Salmo salar smolts performing as well at sea as their naturally produced conspecifics

Large-effect loci mediate rapid adaptation of salmon body size after river regulation

Understanding the potential of natural populations to adapt to altered environments is becoming increasingly relevant in evolutionary research. Currently, our understanding of adaptation to human alteration of the environment is hampered by lack of knowledge on the genetic basis of traits, lack of time series, and little or no information on changes in optimal trait values. Here, we used time series data spanning nearly a century to investigate how the body mass of Atlantic salmon (Salmo salar) adapts to river regulation. We found that the change in body mass followed the change in waterflow, both decreasing to ∼1/3 of their original values. Allele frequency changes at two loci in the regions of vgll3 and six6 predicted more than 80% of the observed body mass reduction. Modeling the adaptive dynamics revealed that the population mean lagged behind its optimum before catching up approximately six salmon generations after the initial waterflow reduction. Our results demonstrate rapid adaptation mediated by large-effect loci and provide insight into the temporal dynamics of evolutionary rescue following human disturbance.

Expression Analysis in Atlantic Salmon Liver Reveals miRNAs Associated with Smoltification and Seawater Adaptation

Simple Summary

Smoltification is a developmental process that preadapts Atlantic salmon for a life in seawater. Suboptimal smoltification and poor timing of transfer to seawater is associated with increased mortality. MicroRNAs (miRNAs) are small non-coding genes. They regulate gene expression post-transcriptionally as part of the miRNA induce silencing complex (miRISC) where they guide miRISC to particular mRNAs (target genes). The aim of this study was to identify Atlantic salmon miRNAs expressed in liver that are associated with smoltification and adaptation to seawater as well as to predict their target genes. In total, 62 guide miRNAs were identified, and by their expression patterns they were clustered into three groups. Target gene predictions followed by gene enrichment analysis of the predicted targets indicated that the guide miRNAs were involved in post-transcriptional regulation of important smoltification associated biological processes. Some of these were energy metabolism, protein metabolism and transport, circadian rhythm, stress and immune response. Together, the results indicate that certain miRNAs are involved in the regulation of many of the important changes occurring in the liver during this developmental transition.

Abstract

Optimal smoltification is crucial for normal development, growth, and health of farmed Atlantic salmon in seawater. Here, we characterize miRNA expression in liver to reveal whether miRNAs regulate gene expression during this developmental transition. Expression changes of miRNAs and mRNAs was studied by small-RNA sequencing and microarray analysis, respectively. This revealed 62 differentially expressed guide miRNAs (gDE-miRNAs) that could be divided into three groups with characteristic dynamic expression patterns. Three of miRNA families are known as highly expressed in liver. A rare arm shift was observed during smoltification in the Atlantic salmon-specific novel-ssa-miR-16. The gDE-miRNAs were predicted to target 2804 of the genes revealing expression changes in the microarray analysis. Enrichment analysis revealed that targets were significantly enriched in smoltification-associated biological process groups. These included lipid and cholesterol synthesis, carbohydrate metabolism, protein metabolism and protein transport, immune system genes, circadian rhythm and stress response. The results indicate that gDE-miRNAs may regulate many of the changes associated with this developmental transition in liver. The results pave the way for validation of the predicted target genes and further study of gDE-miRNA and their targets by functional assays.

Frequency of vateritic otoliths and potential consequences for marine survival in hatchery-reared Atlantic salmon

Otoliths are inner-ear structures of all teleost fish with functional importance for hearing and balance. The otoliths usually consist of aragonite, a polymorph of calcium carbonate, but may also take the form partly or entirely of vaterite, a different polymorph of calcium carbonate. Vateritic otoliths occur sporadically in wild fish, but with a higher frequency in hatchery-reared fish. Abnormal otoliths have direct consequences for the inner-ear functions of fish and may be a symptom of environmental stress. In this study, the authors assess the differences in the frequency of abnormal otoliths and degree of abnormality (% vaterite) for different groups of hatchery-reared Atlantic salmon (Salmo salar) smolt and adults. The groups differed in parental broodstock origin (number of generations in hatchery) and treatment temperature. Smolt from the same groups were also released to complete their ocean migration. The otoliths of the returning and recaptured adults were subsequently extracted to assess the difference in frequency and degree of abnormality between the adults and the smolt from corresponding groups. Return rate varied among groups (0.2%-2.6%). The frequency of vateritic otoliths was high (11.4%-64.4%) and differed among smolt groups. The lowest return rates corresponded with the highest frequency of abnormal otoliths for the groups, suggesting that abnormal otoliths may have negative consequences for marine survival. Furthermore, indications of an effect of fast growth on the formation of abnormal otoliths were found for only one of the experimental groups, and for none of the groups after correcting for Type 1 error. This contradicts previous reports, suggesting rapid growth as the main cause of abnormal otoliths. Adult return rates were generally low, but abnormal otoliths were common, with high coverage (% vaterite).

Microbial Ecology of Atlantic Salmon (Salmo salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota

Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, commercial fishing through wild stock enhancements, and aquaculture production. Flowthrough (FT) hatcheries require more water than recirculating aquaculture systems (RAS), which enable up to 99% of their water to be recycled, thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of three Atlantic salmon hatcheries (RAS n = 2, FT n = 1). Gill, skin, and digesta from six juvenile fish along with tank biofilms and water were sampled from tanks in each of the hatcheries (60 fish across 10 tanks) to assess the built environment and mucosal microbiota using 16S rRNA gene sequencing. The water and tank biofilm had more microbial richness than fish mucus, while skin and digesta from RAS fish had 2 times the richness of FT fish. Body sites each had unique microbiomes (P < 0.001) and were influenced by hatchery system type (P < 0.001), with RAS being more similar. A strong association between the tank and fish microbiome was observed. Water and tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin, and digesta communities were more similar to that in the origin tank biofilm than those in all other experimental tanks, suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. Lastly, microbial diversity and mucous cell density were positively associated with fish growth and length. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome, with the skin microbiome as an important intermediate.IMPORTANCE Atlantic salmon, Salmo salar, is the most farmed marine fish worldwide, with an annual production of 2,248 million metric tons in 2016. Salmon hatcheries are increasingly changing from flowthrough toward recirculating aquaculture system (RAS) design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies of hatcheries have focused either on the fish mucosal microbiota or on the built environment microbiota but have not combined the two to understand their interactions. Our study evaluates how the water and tank biofilm microbiota influences the fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and, furthermore, how this can influence fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for beneficial phenotypes.

A question of scale: Replication and the effective evaluation of conservation interventions

Conservation interventions can keep critically endangered species from going extinct and stabilize threatened populations. The species-specific, case-by-case approaches and small sample sizes inherent to applied conservation measures are not well suited to scientific evaluations of outcomes. Debates about whether a method “works” become entrenched in a vote-counting framework. Furthermore, population-level replication is rare but necessary for disentangling the effects of an intervention from other drivers of population change. Turtle headstarting is a conservation tool that has attracted strong opinions but little robust data. Logistical limitations, such as those imposed by the long lives of turtles, have slowed experimental evaluation and constrained the use of replication or experimental controls. Headstarting project goals vary among projects and stakeholders, and success is not always explicitly defined. To facilitate robust evaluations, we provide direction for data collection and reporting to guide the application of conservation interventions in logistically challenging systems. We offer recommendations for standardized data collection that allow their valuable results to contribute to the development of best practices, regardless of the magnitude of the project. An evidence-based and collaborative approach will lead to improved program design and reporting, and will facilitate constructive evaluation of interventions both within and among conservation programs.